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- PDB-3v0u: Crystal Structure of Perakine Reductase, Founder Member of a Nove... -

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Basic information

Entry
Database: PDB / ID: 3v0u
TitleCrystal Structure of Perakine Reductase, Founder Member of a Novel AKR Subfamily with Unique Conformational Changes during NADPH Binding
ComponentsPerakine reductase
KeywordsOXIDOREDUCTASE / Perakine Reductase / AKR superfamily
Function / homology
Function and homology information


perakine reductase / alkaloid metabolic process / aldo-keto reductase (NADPH) activity / cytoplasm
Similarity search - Function
NADP-dependent oxidoreductase domain / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesRauvolfia serpentina (serpentwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.203 Å
AuthorsSun, L. / Chen, Y. / Rajendran, C. / Panjikar, S. / Mueller, U. / Wang, M. / Rosenthal, C. / Mindnich, R. / Penning, T.M. / Stoeckigt, J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal structure of perakine reductase, founding member of a novel aldo-keto reductase (AKR) subfamily that undergoes unique conformational changes during NADPH binding.
Authors: Sun, L. / Chen, Y. / Rajendran, C. / Mueller, U. / Panjikar, S. / Wang, M. / Mindnich, R. / Rosenthal, C. / Penning, T.M. / Stockigt, J.
History
DepositionDec 8, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Perakine reductase


Theoretical massNumber of molelcules
Total (without water)37,4611
Polymers37,4611
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Perakine reductase

A: Perakine reductase


Theoretical massNumber of molelcules
Total (without water)74,9222
Polymers74,9222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1540 Å2
ΔGint-11 kcal/mol
Surface area25050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.102, 93.650, 143.077
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Perakine reductase


Mass: 37460.953 Da / Num. of mol.: 1 / Mutation: A213W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rauvolfia serpentina (serpentwood) / Gene: PR / Production host: Escherichia coli (E. coli) / References: UniProt: Q3L181
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.65 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→71.5 Å / Num. obs: 20584 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.1_743) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PZ0

1pz0


Resolution: 2.203→40.634 Å / SU ML: 0.58 / σ(F): 2.01 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2474 960 5 %
Rwork0.2123 --
all0.24 --
obs0.2141 19198 95.37 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.957 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.1496 Å20 Å2-0 Å2
2--1.041 Å20 Å2
3----6.1906 Å2
Refinement stepCycle: LAST / Resolution: 2.203→40.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 0 69 2257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082229
X-RAY DIFFRACTIONf_angle_d1.0933016
X-RAY DIFFRACTIONf_dihedral_angle_d16.294837
X-RAY DIFFRACTIONf_chiral_restr0.071345
X-RAY DIFFRACTIONf_plane_restr0.005387
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.203-2.31910.30731170.3064224084
2.3191-2.46440.31611360.2666258196
2.4644-2.65470.31141400.2625266198
2.6547-2.92170.29481420.23268699
2.9217-3.34440.30711400.2095267399
3.3444-4.21280.22681420.1802268697
4.2128-40.64110.19611430.1987271195
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.482-0.68380.99893.5482-0.50954.61160.0839-0.2502-0.15870.1410.09870.23170.8421-0.2602-0.16950.403-0.02340.00010.21340.0080.2569-2.680918.867316.9878
23.2947-1.46180.39295.1323-0.80233.1348-0.2695-0.17230.19080.41730.2281-0.0604-0.4528-0.04590.030.28880.0530.01330.27080.0320.329-2.266640.610312.6418
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 0:169)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 170:310)

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